From: yxiong_at_mail.ccnu.edu.cn
Date: Wed Dec 24 2003 - 03:44:58 CST
Dear sir,
When I did a MD at 40000 step, the NAMD program terminated abnormally. I got the
following information:
-------------------------------------------------------------------------
WRITING COORDINATES TO DCD FILE AT STEP 41500
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
Stack Traceback:
[0] _ZN9HomePatch13doMarginCheckEv+0x202 [0x81d702e]
[1] _ZN9HomePatch14positionsReadyEi+0x7b [0x81d5ab7]
[2] _ZN9Sequencer17runComputeObjectsEii+0xec [0x822c1b0]
[3] _ZN9Sequencer9integrateEv+0x69f [0x822f2a7]
[4] _ZN9Sequencer9algorithmEv+0x158 [0x822ba80]
[5] _ZN9Sequencer9threadRunEPS_+0xc [0x82386b4]
[6] /home/xiong/NAMD/namd2 [0x82758a4]
[7] Charm++ Runtime: Converse thread (qt_args+0x66 [0x82c40aa])-
----------------------------------------------------------------------------
It seems that I need solve this problem by modifing margin or disable
useFlexibleCell. However when I set margin to 2, it still can't solve it. Moreover
I am so surprised that in fact I had set useFlexibleCell disable in old
configuration file,
------------------------------------------------------
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
-------------------------------------------------------
but I found the cellsize became smaller and smaller in *.xsc file. Why can
"useFlexibleCell no" not work?
-----------------------------------------------------------------------
38000 59.5493 0 0 0 62.9521 0 0 0 64.6536 43.87 -1.73 27.2 0.000104506 0.000104506
0.000104506 0
0 0
38500 59.4916 0 0 0 62.8911 0 0 0 64.5909 43.87 -1.73 27.2 -4.48954e-07
-4.48954e-07 -4.48954e-0
7 0 0 0
39000 59.4441 0 0 0 62.8409 0 0 0 64.5393 43.87 -1.73 27.2 -5.16266e-07
-5.16266e-07 -5.16266e-0
7 0 0 0
39500 59.3816 0 0 0 62.7748 0 0 0 64.4715 43.87 -1.73 27.2 -2.24862e-05
-2.24862e-05 -2.24862e-0
5 0 0 0
40000 59.1866 0 0 0 62.5687 0 0 0 64.2598 43.87 -1.73 27.2 8.71611e-06 8.71611e-06
8.71611e-06 0
0 0
40500 59.0098 0 0 0 62.3818 0 0 0 64.0678 43.87 -1.73 27.2 2.63917e-06 2.63917e-06
2.63917e-06 0
0 0
41000 59.0242 0 0 0 62.397 0 0 0 64.0834 43.87 -1.73 27.2 -3.55531e-05
-3.55531e-05 -3.55531e-05
0 0 0
41500 59.0253 0 0 0 62.3982 0 0 0 64.0847 43.87 -1.73 27.2 1.10309e-05 1.10309e-05
1.10309e-05 0
0 0
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